Docker-compose definition

.dockerignore

@@ -1,5 +1,4 @@
 */bin/
-*/obj/
 */out/
 */.vs
 .vscode

containerize_leaf.sh

@@ -1,3 +1,4 @@
+set -e
 
 # Set configurable stuff
 SA_PASSWORD=Th3PA55--8zz       # DB password
@@ -15,7 +16,7 @@ if [ -z ${LEAF_JWT_KEY+x}    ]; then echo "LEAF_JWT_KEY is unset!"    exit; fi
 if [ -z ${LEAF_JWT_KEY_PW+x} ]; then echo "LEAF_JWT_KEY_PW is unset!" exit; fi
 
 # Extract cert/key path from ENVs
-KEYS_PATH=`echo $LEAF_JWT_CERT | sed 's/\/cert.pem.*//'`
+KEYS_PATH=$(dirname "$LEAF_JWT_CERT")
 if [ -z ${KEYS_PATH+x} ]; then echo "Couldn't find cert+key path! Are you sure LEAF_JWT_CERT is a valid path?" && exit; fi
 
 #--------------
@@ -25,7 +26,7 @@ docker run -d -e "ACCEPT_EULA=Y" -e "SA_PASSWORD=$SA_PASSWORD" -p 1433:1433 \
                 -v leaf_sqlvolume:/var/opt/mssql \
                 --name leaf_db_demo mcr.microsoft.com/mssql/server:2017-latest 
 
-sleep 10s
+sleep 10
 
 docker_sqlcmd() {
     path="$1"
@@ -36,7 +37,7 @@ docker_sqlcmd() {
       /opt/mssql-tools/bin/sqlcmd -S 'host.docker.internal' -U SA -P "$SA_PASSWORD" "$@" -i /sql/"$path"
 }
 
-docker_getDbs(){
+docker_getDbs() {
   docker run --rm \
          -v "$PWD"/src/db/build/:/sql \
          mcr.microsoft.com/mssql-tools \
@@ -67,6 +68,7 @@ docker run \
     -e "LEAF_APP_DB=Server=$DB_SERVER,1433;Database=LeafDB;uid=sa;Password=$SA_PASSWORD" \
     -e "LEAF_CLIN_DB=Server=$DB_SERVER,1433;Database=TestDB;uid=sa;Password=$SA_PASSWORD" \
     -e "LEAF_JWT_KEY_PW=$LEAF_JWT_KEY_PW" \
+    -e "UnsecuredIsAdmin"="true" \
     -p 5001:5001 \
     -v ${PWD}/src/server:/app \
     -v ${KEYS_PATH}:/.keys \

src/db/build/Dockerfile

@@ -1,12 +1,11 @@
-FROM microsoft/mssql-server-linux:2017-latest
+FROM mcr.microsoft.com/mssql/server:2017-latest
 
 ARG sapw
 
 RUN mkdir data
 
 # Include schema and initial data
-COPY ./LeafDB.sql ./LeafDB.Data.sql ./LeafDB.Exec.sql ./SynPuf_OMOP.Restore.sql ./SynPuf_OMOP.Shrink.sql ./
-COPY ./SynPuf_OMOP.bak ./data/
+COPY ./LeafDB.sql ./LeafDB.Init.sql ./TestDB.sql ./
 
 # Accept EULA
 ENV ACCEPT_EULA Y
@@ -20,10 +19,6 @@ VOLUME /bak
 # Set up database
 RUN /opt/mssql/bin/sqlservr & sleep 10 \
     && /opt/mssql-tools/bin/sqlcmd -S localhost -U SA -P ${MSSQL_SA_PASSWORD} -i ./LeafDB.sql \
-    && /opt/mssql-tools/bin/sqlcmd -S localhost -U SA -P ${MSSQL_SA_PASSWORD} -i ./LeafDB.Data.sql \
-    && /opt/mssql-tools/bin/sqlcmd -S localhost -U SA -P ${MSSQL_SA_PASSWORD} -i ./LeafDB.Exec.sql \
-    && /opt/mssql-tools/bin/sqlcmd -S localhost -U SA -P ${MSSQL_SA_PASSWORD} -i ./SynPuf_OMOP.Restore.sql \
-    && /opt/mssql-tools/bin/sqlcmd -S localhost -U SA -P ${MSSQL_SA_PASSWORD} -i ./SynPuf_OMOP.Shrink.sql \
-    && pkill sqlservr
-
-RUN rm /data/SynPuf_OMOP.bak
+    && /opt/mssql-tools/bin/sqlcmd -S localhost -U SA -P ${MSSQL_SA_PASSWORD} -i ./LeafDB.Init.sql -d LeafDB \
+    && /opt/mssql-tools/bin/sqlcmd -S localhost -U SA -P ${MSSQL_SA_PASSWORD} -i ./TestDB.sql \
+    && pkill sqlservr

src/db/build/TestDB.sql

@@ -5,247 +5,4 @@ GO
  * TestDB
  */
 CREATE DATABASE [TestDB]
-GO
-
-ALTER DATABASE [TestDB] SET RECOVERY SIMPLE
-GO
-
-USE [TestDB]
-GO
-
-SET ANSI_NULLS ON
-GO
-SET QUOTED_IDENTIFIER ON
-GO
-CREATE TABLE [dbo].[person](
-	[person_id] [int] NULL,
-	[age] [int] NULL,
-	[gender] [nvarchar](20) NULL
-) ON [PRIMARY]
-GO
-
-SET ANSI_NULLS ON
-GO
-SET QUOTED_IDENTIFIER ON
-GO
-CREATE TABLE [dbo].[visit_occurrence](
-	[person_id] [int] NULL,
-	[visit_occurrence_id] [int] NULL,
-	[visit_date] [datetime] NULL,
-	[visit_type] [nvarchar](10) NULL
-) ON [PRIMARY]
-GO
-
-INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (1, 28, N'F')
-GO
-INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (2, 74, N'M')
-GO
-INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (3, 55, N'M')
-GO
-INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (4, 43, N'F')
-GO
-INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (5, 99, N'F')
-GO
-INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (1, 100, CAST(N'2020-08-14T00:00:00.000' AS DateTime), N'IP')
-GO
-INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (1, 101, CAST(N'2020-09-22T00:00:00.000' AS DateTime), N'OP')
-GO
-INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (2, 102, CAST(N'2018-06-01T00:00:00.000' AS DateTime), N'IP')
-GO
-INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (2, 103, CAST(N'2018-02-28T00:00:00.000' AS DateTime), N'ED')
-GO
-INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (3, 104, CAST(N'2015-01-01T00:00:00.000' AS DateTime), N'OP')
-GO
-INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (4, 105, CAST(N'2022-09-19T00:00:00.000' AS DateTime), N'OP')
-GO
-INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (4, 106, CAST(N'2028-01-01T00:00:00.000' AS DateTime), N'IP')
-GO
-
-USE [LeafDB]
-GO
-
-
-DECLARE @user NVARCHAR(20) = 'TestDB.sql'
-DECLARE @yes BIT = 1
-DECLARE @no  BIT = 0
-
-INSERT INTO app.ConceptSqlSet (SqlSetFrom, IsEncounterBased, IsEventBased, SqlFieldDate, Created, CreatedBy, Updated, UpdatedBy)
-SELECT *
-FROM (VALUES ('dbo.person',               @no,  @no,  NULL,          GETDATE(), @user, GETDATE(), @user),                          
-             ('dbo.visit_occurrence',     @yes, @no, '@.visit_date', GETDATE(), @user, GETDATE(), @user)
-     ) AS X(col1,col2,col3,col4,col5,col6,col7,col8)
-
-DECLARE @sqlset_person           INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.person')
-DECLARE @sqlset_visit_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.visit_occurrence')
-
-INSERT INTO app.Concept (ExternalId, ExternalParentId, [IsNumeric], IsParent, IsRoot, SqlSetId, SqlSetWhere, 
-                         SqlFieldNumeric, UiDisplayName, UiDisplayText, UiDisplayUnits, UiNumericDefaultText, UiDisplayPatientCount)
-SELECT ExternalId            = 'A'
-     , ExternalParentId      = NULL
-     , [IsNumeric]           = @no
-     , IsParent              = @yes
-     , IsRoot                = @yes
-     , SqlSetId              = @sqlset_person
-     , SqlSetWhere           = NULL
-     , SqlFieldNumeric       = NULL
-     , UiDisplayName         = 'Demographics'
-     , UiDisplayText         = 'Have demographics'
-     , UiDisplayUnits        = NULL
-     , UiNumericDefaultText  = NULL
-     , UiDisplayPatientCount  = (SELECT COUNT(*) FROM TestDB.dbo.person)
-UNION ALL                          
-SELECT ExternalId            = 'A1'
-     , ExternalParentId      = 'A'
-     , [IsNumeric]           = @no
-     , IsParent              = @yes
-     , IsRoot                = @no
-     , SqlSetId              = @sqlset_person
-     , SqlSetWhere           = '@.gender IS NOT NULL'
-     , SqlFieldNumeric       = NULL
-     , UiDisplayName         = 'Gender'
-     , UiDisplayText         = 'Identify with a gender'
-     , UiDisplayUnits        = NULL
-     , UiNumericDefaultText  = NULL
-     , UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.person)
-UNION ALL    
-SELECT ExternalId            = 'A11'
-     , ExternalParentId      = 'A1'
-     , [IsNumeric]           = @no
-     , IsParent              = @no
-     , IsRoot                = @no
-     , SqlSetId              = @sqlset_person
-     , SqlSetWhere           = '@.gender = ''F'''
-     , SqlFieldNumeric       = NULL
-     , UiDisplayName         = 'Female'
-     , UiDisplayText         = 'Identify as Female'
-     , UiDisplayUnits        = NULL
-     , UiNumericDefaultText  = NULL
-     , UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.person WHERE gender = 'F')
-UNION ALL                          
-SELECT ExternalId            = 'A12'
-     , ExternalParentId      = 'A1'
-     , [IsNumeric]           = @no
-     , IsParent              = @no
-     , IsRoot                = @no
-     , SqlSetId              = @sqlset_person
-     , SqlSetWhere           = '@.gender = ''M'''
-     , SqlFieldNumeric       = NULL
-     , UiDisplayName         = 'Male'
-     , UiDisplayText         = 'Identify as Male'
-     , UiDisplayUnits        = NULL
-     , UiNumericDefaultText  = NULL
-     , UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.person WHERE gender = 'M')
-UNION ALL                          
-SELECT ExternalId            = 'A2'
-     , ExternalParentId      = 'A'
-     , [IsNumeric]           = @yes
-     , IsParent              = @no
-     , IsRoot                = @no
-     , SqlSetId              = @sqlset_person
-     , SqlSetWhere           = '@.age IS NOT NULL'
-     , SqlFieldNumeric       = '@.age'
-     , UiDisplayName         = 'Age'
-     , UiDisplayText         = 'Are currently'
-     , UiDisplayUnits        = 'years of age'
-     , UiNumericDefaultText  = 'any age'
-     , UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.person WHERE age IS NOT NULL)
-UNION ALL                          
-SELECT ExternalId            = 'B'
-     , ExternalParentId      = NULL
-     , [IsNumeric]           = @no
-     , IsParent              = @yes
-     , IsRoot                = @yes
-     , SqlSetId              = @sqlset_visit_occurrence
-     , SqlSetWhere           = NULL
-     , SqlFieldNumeric       = NULL
-     , UiDisplayName         = 'Encounters'
-     , UiDisplayText         = 'Had an encounter'
-     , UiDisplayUnits        = NULL
-     , UiNumericDefaultText  = NULL
-     , UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.visit_occurrence)     
-UNION ALL                          
-SELECT ExternalId            = 'B1'
-     , ExternalParentId      = 'B'
-     , [IsNumeric]           = @no
-     , IsParent              = @no
-     , IsRoot                = @no
-     , SqlSetId              = @sqlset_visit_occurrence
-     , SqlSetWhere           = NULL
-     , SqlFieldNumeric       = NULL
-     , UiDisplayName         = 'Inpatient'
-     , UiDisplayText         = 'Had an Inpatient encounter'
-     , UiDisplayUnits        = NULL
-     , UiNumericDefaultText  = NULL
-     , UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.visit_occurrence WHERE visit_type = 'IP')     
-UNION ALL     
-SELECT ExternalId            = 'B2'
-     , ExternalParentId      = 'B'
-     , [IsNumeric]           = @no
-     , IsParent              = @no
-     , IsRoot                = @no
-     , SqlSetId              = @sqlset_visit_occurrence
-     , SqlSetWhere           = NULL
-     , SqlFieldNumeric       = NULL
-     , UiDisplayName         = 'Outpatient'
-     , UiDisplayText         = 'Had an Outpatient encounter'
-     , UiDisplayUnits        = NULL
-     , UiNumericDefaultText  = NULL
-     , UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.visit_occurrence WHERE visit_type = 'OP')     
-UNION ALL     
-SELECT ExternalId            = 'B3'
-     , ExternalParentId      = 'B'
-     , [IsNumeric]           = @no
-     , IsParent              = @no
-     , IsRoot                = @no
-     , SqlSetId              = @sqlset_visit_occurrence
-     , SqlSetWhere           = NULL
-     , SqlFieldNumeric       = NULL
-     , UiDisplayName         = 'Emergency'
-     , UiDisplayText         = 'Had an Emergency Department encounter'
-     , UiDisplayUnits        = NULL
-     , UiNumericDefaultText  = NULL
-     , UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.visit_occurrence WHERE visit_type = 'ED')     
-
-
-
-/**
-* Set ParentId based on ExternalIds
-*/
-UPDATE LeafDB.app.Concept
-SET ParentId = P.Id
-FROM LeafDB.app.Concept AS C
-    INNER JOIN (SELECT P.Id, P.ParentId, P.ExternalId
-                FROM LeafDB.app.Concept AS P) AS P
-                    ON C.ExternalParentID = P.ExternalID
-WHERE C.ParentId IS NULL
-
-/**
-* Set RootIds
-*/
-; WITH roots AS
-(
-    SELECT RootId            = C.Id
-        , RootUiDisplayName = C.UiDisplayName
-        , C.IsRoot
-        , C.Id
-        , C.ParentId
-        , C.UiDisplayName
-    FROM LeafDB.app.Concept AS C
-    WHERE C.IsRoot = 1
-    UNION ALL
-    SELECT roots.RootId
-        , roots.RootUiDisplayName
-        , C2.IsRoot
-        , C2.Id
-        , C2.ParentId
-        , C2.UiDisplayName
-    FROM roots
-        INNER JOIN LeafDB.app.Concept AS C2
-            ON C2.ParentId = roots.Id
-)
-UPDATE LeafDB.app.Concept
-SET RootId = roots.RootId
-FROM LeafDB.app.Concept AS C
-    INNER JOIN roots
-        ON C.Id = roots.Id
-WHERE C.RootId IS NULL
+GO

src/docker-compose.yml

@@ -0,0 +1,53 @@
+version: '3'
+services:
+
+  db:
+    build:
+      context: ./db/build
+      args:
+        - sapw=${SA_PASSWORD}
+    image: leaf_db
+    container_name: leaf_db_demo
+    ports:
+      - 1433:1433
+    restart: always
+    networks:
+      - leaf
+
+  server:
+    build: ./server
+    image: leaf_api
+    container_name: leaf_api_demo
+    volumes:
+      - server-log:/logs
+    environment:
+      - LEAF_APP_DB=${LEAF_APP_DB}
+      - LEAF_CLIN_DB=${LEAF_CLIN_DB}
+      - LEAF_JWT_KEY_PW=${LEAF_JWT_KEY_PW}
+      - UnsecuredIsAdmin=${UnsecuredIsAdminProd}
+    restart: always
+    networks:
+      - leaf
+    depends_on:
+      - db
+
+  ui-client:
+    build:
+      context: ./ui-client
+    container_name: leaf_ui
+    ports:
+      - 80:80
+    restart: always
+    networks:
+      - leaf
+    stdin_open: true
+    depends_on:
+      - db
+      - server
+
+networks:
+  leaf:
+
+
+volumes:
+  server-log:

src/server/.dockerignore

@@ -1,4 +0,0 @@
-**/bin/
-**/obj/
-out/
-.vs